Getting Data into Galaxy

Data Upload

Use the Upload tool to load datasets into your history


  • Files from your computer using Choose local files
  • Files with a public URL using Paste/Fetch data
  • Files from remote data sources using Choose remote files

:flashlight: files can be dragged and dropped to launch the Upload tool!

More choices include

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  • Use a data retrieval tool to load files into your history. See the tool panel for these options
  • Copy datasets from Data → Data Libraries into your history

Batch Upload

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All servers support a resume function directly through the Upload tool for very large local data loading.

Data retrieved through all other methods is entirely remote and performance is dependent on the connection between that other service and the Galaxy server where you are working. offers the custom command-line galaxy-upload function.

FTP Upload is available at some services, including and


:speech_balloon: I tried to retrieve a batch of accessions from NCBI SRA, but the query failed!

First, check your query terms. Most of these underlying tools expect one accession term per line without any extra spaces or blank lines. You can confirm by reviewing the tool form instructions.

Next, try again! External data services can get busy and reject queries for unclear reasons. Trying again at a different time is a common solution.

:books: References

:mechanic: FAQ: What information should I include when reporting a problem?

Any persistent problems can be reported in a new question for community help. Be sure to provide enough context so others can review the situation exactly and quickly offer advice.

Consider FAQ: Sharing your History or posting content from the Job Information :information_source: view as described in FAQ: Troubleshooting errors.